RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy12711
(639 letters)
>3h0g_K DNA-directed RNA polymerase II subunit RPB11; transcription,
multi-protein complex, DNA- binding, magnesium; 3.65A
{Schizosaccharomyces pombe}
Length = 123
Score = 94.7 bits (235), Expect = 2e-23
Identities = 26/89 (29%), Positives = 40/89 (44%)
Query: 104 PNCRTFVFEKEGHTFGSVITHILQSYPEVDFAGYSVPHPADFQIFIRIQVKDGYDSIDIL 163
PN EKE HT +++ + L S V FAGY VPHP + +R+Q + ++
Sbjct: 27 PNAAVVTLEKEDHTLANMLANQLLSDERVLFAGYKVPHPLNHNFILRVQTVEDCSPKQVI 86
Query: 164 KKGIKELESACDRITETFNDAMQCKVILK 192
K L + + I F + K+I
Sbjct: 87 VDAAKSLITHLEEIKVNFMREWELKMISV 115
>1twf_K B13.6, DNA-directed RNA polymerase II 13.6 kDa polypepti;
transcription, mRNA, multiprotein complex; HET: UTP;
2.30A {Saccharomyces cerevisiae} SCOP: d.74.3.2 PDB:
1i3q_K 1i6h_K 1k83_K* 1nik_K 1nt9_K 1pqv_K 1r5u_K
1r9s_K* 1r9t_K* 1sfo_K* 1twa_K* 1twc_K* 1i50_K* 1twg_K*
1twh_K* 1wcm_K 1y1v_K 1y1w_K 1y1y_K 1y77_K* ...
Length = 120
Score = 92.7 bits (230), Expect = 1e-22
Identities = 28/85 (32%), Positives = 39/85 (45%)
Query: 104 PNCRTFVFEKEGHTFGSVITHILQSYPEVDFAGYSVPHPADFQIFIRIQVKDGYDSIDIL 163
PN FEKE HT G++I L + +V FA Y V HP + +RIQ +GYD D L
Sbjct: 28 PNAVVITFEKEDHTLGNLIRAELLNDRKVLFAAYKVEHPFFARFKLRIQTTEGYDPKDAL 87
Query: 164 KKGIKELESACDRITETFNDAMQCK 188
K + + + F +
Sbjct: 88 KNACNSIINKLGALKTNFETEWNLQ 112
>2pa8_L DNA-directed RNA polymerase subunit L; ferredoxin-like Fe-S binding
motif, platform for RNA polymer assembly, transferase;
1.76A {Sulfolobus solfataricus} PDB: 2pmz_L 3hkz_L
2waq_L 2wb1_L 2y0s_L
Length = 92
Score = 91.5 bits (227), Expect = 1e-22
Identities = 22/87 (25%), Positives = 33/87 (37%)
Query: 100 LNVKPNCRTFVFEKEGHTFGSVITHILQSYPEVDFAGYSVPHPADFQIFIRIQVKDGYDS 159
L + N E E HT G++I L+ V FA Y PHP +I ++I
Sbjct: 6 LKSESNYLELEIEGEDHTLGNLIAGTLRRISGVSFASYYQPHPLSDKIIVKILTDGSITP 65
Query: 160 IDILKKGIKELESACDRITETFNDAMQ 186
D L K I+ + + +
Sbjct: 66 KDALLKAIENIRGMTSHYIDEIKGLTK 92
>1xpp_A TA1416, DNA-directed RNA polymerase subunit L; structural genomics,
protein structure initiative, MCSG; 1.60A {Thermoplasma
acidophilum} SCOP: d.74.3.2
Length = 115
Score = 87.3 bits (216), Expect = 8e-21
Identities = 17/87 (19%), Positives = 34/87 (39%), Gaps = 1/87 (1%)
Query: 100 LNVKPNCRTFVFEKEGHTFGSVITHILQSYPEVDFAGYSVPHPADFQIFIRIQVKDGYDS 159
++ + N T +T + + +VD A Y + HP I ++VK G
Sbjct: 16 ISKEKNSITVEMINYDNTLLRTLVEEILKDDQVDEARYYIKHPVIDNPQIYVRVKSG-KP 74
Query: 160 IDILKKGIKELESACDRITETFNDAMQ 186
+K+ +++L + + F Q
Sbjct: 75 QSAIKRAVRKLSKLYEDLGTQFQKEFQ 101
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 70.7 bits (172), Expect = 8e-13
Identities = 90/684 (13%), Positives = 199/684 (29%), Gaps = 225/684 (32%)
Query: 2 LIEYLDSKILKKYRFQLFHSERQDNTSSTSTSIHRSKVQVQLLYMTEEQQLKPGLEQWCF 61
++ D K ++ + E D+ + ++ + L+ T + + ++++
Sbjct: 29 FVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTL----RLFWTLLSKQEEMVQKF-- 82
Query: 62 CFSIPTSTSSVNTSLCINY---MESKQLENSSPVWELRDNTLNVKPNCRTFVFEKEGHTF 118
V L INY M + E P R ++ +++
Sbjct: 83 ----------VEEVLRINYKFLMSPIKTEQRQP-----------SMMTRMYIEQRD---- 117
Query: 119 GSVITHILQSYPEVDFAGYSVPHPADFQIFIRIQVKDGYDSIDILKKGIKELESACDRIT 178
L + +V FA Y+V R+Q L++ + EL A +
Sbjct: 118 ------RLYNDNQV-FAKYNVS---------RLQ------PYLKLRQALLELRPAKN--- 152
Query: 179 ETFNDAMQCKVIL-------KLTLLVIQKASKNLRV----------LVIGSQKHS----- 216
V++ K T + + + +V L + +
Sbjct: 153 ----------VLIDGVLGSGK-TWVALD-VCLSYKVQCKMDFKIFWLNLKNCNSPETVLE 200
Query: 217 MMQ--CRNMDSNHDVEKYRYEDSMDYIKIPIEAIRPKTRQVLNDK--------LCDI--K 264
M+Q +D N D IK+ I +I+ + R++L K L ++
Sbjct: 201 MLQKLLYQIDPNWTSR----SDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNA 256
Query: 265 QLMSPENYQ-------RDYRGLADLMDIKAPPNPNCEDL--------MKKMFEDW--TKS 307
+ + N R + + D + + + + +K + + +
Sbjct: 257 KAWNAFNLSCKILLTTRF-KQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRP 315
Query: 308 STLDRSVFN--------IATFLHFLECIDRFDVYDDCIGFIEEDCLYYENTRLGNSISKN 359
L R V IA + + + +D + + +L I
Sbjct: 316 QDLPREVLTTNPRRLSIIAESIR--DGLATWDNW-----------KHVNCDKLTTIIE-- 360
Query: 360 GACMD--DPSVITIEDVKSLNLGCGLAHYDAL---------------LLYDEADFDLAKQ 402
+ ++ +P + + +D L L++ +
Sbjct: 361 -SSLNVLEP-----AEYR--------KMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMV 406
Query: 403 FNTQLNKMGFTVCDKDNSFLTGQFEHSAFIQVMDRCTCVIVLMSTHFMNNSLLHS--LTQ 460
+L+K +++ +K T I + + + + N LH +
Sbjct: 407 VVNKLHK--YSLVEKQPKEST--------ISIPS----IYLELKVKLENEYALHRSIVDH 452
Query: 461 YAEAKHIDHTIHSKIIPILCSDDYFSVGFLQYCVKLKLNHYASNMEQ-----FWDRLYYS 515
Y K D I P L D Y F + + H+ N+E + ++
Sbjct: 453 YNIPKTFDS--DDLIPPYL--DQY----FYSH-----IGHHLKNIEHPERMTLFRMVFLD 499
Query: 516 LKGVGK-----GVPEWDFASNMEQFWD-RLY--YSLKGVGKGSQ--KQAIQFQTTPTSMP 565
+ + + S + + Y Y K + + F
Sbjct: 500 FRFLEQKIRHDSTAWNASGSILNTLQQLKFYKPYICDNDPKYERLVNAILDFLPKIEENL 559
Query: 566 VAPPDYTLSQQAVAPPDYTLPQQA 589
+ L + A+ D + ++A
Sbjct: 560 ICSKYTDLLRIALMAEDEAIFEEA 583
Score = 47.2 bits (111), Expect = 2e-05
Identities = 44/299 (14%), Positives = 102/299 (34%), Gaps = 65/299 (21%)
Query: 222 NMDSNHDVEKYRYEDSM-----DYIK-IPIEAIRPKTRQVLNDKLCDIKQLMSPENYQRD 275
+MD +Y+Y+D + ++ + ++ + +L+ + D +MS +
Sbjct: 6 HMDFETGEHQYQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEID-HIIMSKDAVSGT 64
Query: 276 YRGLADLMDIKAPPNPNCEDLMKKMFED-------WTKSSTLDRSVFNIATFLHFLECID 328
R L + K E++++K E+ + S ++E D
Sbjct: 65 LR-LFWTLLSKQ------EEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRD 117
Query: 329 RFDVYDDCIGFIEEDCLYYENTRLGNSIS-KNGACMDDPSV-ITIEDVKSLNLGCG---L 383
R +Y+D F + Y +RL + + P+ + I+ V G G +
Sbjct: 118 R--LYNDNQVFAK-----YNVSRLQPYLKLRQALLELRPAKNVLIDGVL----GSGKTWV 166
Query: 384 AHYDALLLYDEADFDLAKQFNTQLNKMGFTVCDKDNSF------LTGQFEHSAFIQVMDR 437
A D L + + + + ++ + C+ + L Q + + + D
Sbjct: 167 A-LDVCL-----SYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPN-WTSRSDH 219
Query: 438 CTCVIVLMSTHFMNNSL--LHSLTQYAEAKHI-DHTIHSKIIPILCSDDYFSVGFLQYC 493
+ + + H + L L Y + + ++K + F++ C
Sbjct: 220 SSNIK--LRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAW------NAFNLS----C 266
Score = 44.1 bits (103), Expect = 1e-04
Identities = 82/554 (14%), Positives = 159/554 (28%), Gaps = 151/554 (27%)
Query: 167 IKELESACDRITETFNDA----MQCKVILKLTLLVIQKASKNLRVLVIGSQKHSMMQCRN 222
E + I F DA CK + + ++ K + I K ++
Sbjct: 11 TGEHQYQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEE----IDHIIMSKDAVSGTLR 66
Query: 223 M-----DSNHDVEKYRYEDSM--DY----IKIPIEAIRPKTRQVL----NDKLCDIKQLM 267
+ ++ + E+ + +Y I E +P + D+L + Q+
Sbjct: 67 LFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVF 126
Query: 268 SPENYQR--DYRGLAD-LMDIKAPPNPNCEDL----MK---KMFEDWTKSSTLDRSVFNI 317
+ N R Y L L++++ P N + + K + + V
Sbjct: 127 AKYNVSRLQPYLKLRQALLELR--PAKN---VLIDGVLGSGK--------TWVALDVCLS 173
Query: 318 ATFLHFLECIDRFDVYDDCIGFIEEDCLYYEN-TRLGNSISKNGACMDDPSV---ITIED 373
++ F ++ + E +L I N D S + I
Sbjct: 174 YKVQCKMD----FKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHS 229
Query: 374 VKS--LNLGCGLAHYDALLLYDE-ADFDLAKQFNTQLNKMGFTVCDKDNSFLTGQFEHSA 430
+++ L + + LL+ + FN C LT +
Sbjct: 230 IQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLS--------C---KILLT-----TR 273
Query: 431 FIQVMDRCTCVIVLMSTHFMNNSLLHSLTQYAE-----AKHIDHTIHS------KIIPIL 479
F QV D + +TH + +LT E K++D P
Sbjct: 274 FKQVTDF---LSAATTTHISLDHHSMTLTP-DEVKSLLLKYLDCRPQDLPREVLTTNPRR 329
Query: 480 CS-------------DDYFSVGF--LQYCVKLKLNHYASNMEQFWDRLYYSL----KGVG 520
S D++ V L ++ LN + +++ L
Sbjct: 330 LSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYR---KMFDRLSVFPPSA- 385
Query: 521 KGVPE------WDFAS--NMEQFWDRLY-YSLKGVGKGSQKQA-----IQFQTTPTSMPV 566
+P W ++ ++L+ YSL V K ++ I +
Sbjct: 386 -HIPTILLSLIWFDVIKSDVMVVVNKLHKYSL--VEKQPKESTISIPSIYLELKVK---- 438
Query: 567 APPDYTLSQQAVAPPDYTLPQQATNSQSITNNMS----------------EEKKDSMKKP 610
+Y L + V Y +P+ + I + E+ +
Sbjct: 439 LENEYALHRSIVD--HYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMV 496
Query: 611 MLMLT-LQNGIRNT 623
L L+ IR+
Sbjct: 497 FLDFRFLEQKIRHD 510
>3ub2_A TOLL/interleukin-1 receptor domain-containing ADA protein; TIR
domain, TLRS adaptor, immune system; 2.40A {Homo
sapiens} PDB: 3ub3_A 3ub4_A 2y92_A
Length = 146
Score = 60.5 bits (147), Expect = 4e-11
Identities = 18/134 (13%), Positives = 43/134 (32%), Gaps = 9/134 (6%)
Query: 386 YDALLLYDEADFDLAKQFNTQL--NKMGFTVCDKDNSFLTGQFEHSAFIQVMDRCTCVIV 443
YD + + E D A+ + L + + G S Q + C ++
Sbjct: 11 YDVCVCHSEEDLVAAQDLVSYLEGSTASLRCFLQLRDATPGGAIVSELCQALSSSHCRVL 70
Query: 444 LMSTHFMNNSLLHSLTQYAEAKHIDHTIHSKIIPILCSDDYFSV-GFLQYCVKLKLNHYA 502
L++ F+ + Q +A IP+L + L++ +
Sbjct: 71 LITPGFLQDPW--CKYQMLQALTEAPGAEGCTIPLLSGLSRAAYPPELRFMYYVDGR--- 125
Query: 503 SNMEQFWDRLYYSL 516
+ + ++ ++
Sbjct: 126 -GPDGGFRQVKEAV 138
>3mop_A Myeloid differentiation primary response protein; death domain
complex, helical symmetry, single-stranded HELI
assembly; 3.40A {Homo sapiens}
Length = 110
Score = 58.7 bits (142), Expect = 7e-11
Identities = 23/114 (20%), Positives = 43/114 (37%), Gaps = 26/114 (22%)
Query: 243 IPIEAIRPKTRQVLNDKLCDIKQLMSPEN-YQRDYRGLADLMD--------IKAPPNPNC 293
+P+ A+ + R+ +L ++ D+ LA+ MD ++ +P
Sbjct: 2 LPLAALNMRVRR----RLS---LFLNVRTQVAADWTALAEEMDFEYLEIRQLETQADP-- 52
Query: 294 EDLMKKMFEDWTKSSTLDRSVFNIATFLHFLECIDRFDVYDDCIGFIEEDCLYY 347
++ + W R ++ L L + R DV + IEEDC Y
Sbjct: 53 ---TGRLLDAWQG-----RPGASVGRLLELLTKLGRDDVLLELGPSIEEDCQKY 98
>2js7_A Myeloid differentiation primary response protein MYD88;
MYD88_human, TIR domain, TOLL like receptor adaptor
domain, innate immune signaling; NMR {Homo sapiens} PDB:
2z5v_A
Length = 160
Score = 58.2 bits (141), Expect = 3e-10
Identities = 26/136 (19%), Positives = 51/136 (37%), Gaps = 6/136 (4%)
Query: 386 YDALLLYDEADFDLAKQFNTQL--NKMGFTVCDKDNSFLTGQFEHSAFIQ-VMDRCTCVI 442
+DA + Y +D ++ QL +C D L G S + + RC ++
Sbjct: 17 FDAFICYCPSDIQFVQEMIRQLEQTNYRLKLCVSDRDVLPGTCVWSIASELIEKRCRRMV 76
Query: 443 VLMSTHFMNNSLLHSLTQYAEAKHIDHTIHSKIIPILCSD-DYFSVGFLQYCVKLKLNHY 501
V++S ++ + T++A + ++IPI L++ +
Sbjct: 77 VVVSDDYLQSKECDFQTKFALSLSPGAH-QKRLIPIKYKAMKKEFPSILRFITVCDYTNP 135
Query: 502 ASNMEQFWDRLYYSLK 517
+ FW RL +L
Sbjct: 136 CTK-SWFWTRLAKALS 150
>2j67_A TOLL like receptor 10; TIR, IL-1, TLR10, membrane, innate immunity,
immune response, leucine-rich repeat, glycoprotein,
transmembrane; 2.20A {Homo sapiens} PDB: 1fyv_A
Length = 178
Score = 51.8 bits (124), Expect = 6e-08
Identities = 24/144 (16%), Positives = 44/144 (30%), Gaps = 13/144 (9%)
Query: 385 HYDALLLYDEADFDL-AKQFNTQL--NKMGFTVCDKDNSFLTGQFEHSAFIQVMDRCTCV 441
+ A + Y E D + L +C ++ F G+ + +++
Sbjct: 35 RFHAFISYSEHDSLWVKNELIPNLEKEDGSILICLYESYFDPGKSISENIVSFIEKSYKS 94
Query: 442 IVLMSTHFMNNSLLHSLTQYAEAKHIDHTIHSKIIPILCSDDYFSV---------GFLQY 492
I ++S +F+ N H +A II IL F L+
Sbjct: 95 IFVLSPNFVQNEWCHYEFYFAHHNLFHEN-SDHIILILLEPIPFYCIPTRYHKLKALLEK 153
Query: 493 CVKLKLNHYASNMEQFWDRLYYSL 516
L+ FW L ++
Sbjct: 154 KAYLEWPKDRRKCGLFWANLRAAI 177
>1t3g_A X-linked interleukin-1 receptor accessory protein-like 1; TIR,
IL-1RAPL, IL-1R, TLR, membrane protein; 2.30A {Homo
sapiens}
Length = 159
Score = 51.6 bits (123), Expect = 6e-08
Identities = 29/155 (18%), Positives = 55/155 (35%), Gaps = 24/155 (15%)
Query: 386 YDALLLYDEADFDLAKQFNTQL-------------NKMGFTVCDKDNSFLTGQFEHSAFI 432
YDA L Y + D D Q + G+ + D +
Sbjct: 3 YDAYLSYTKVDPDQWNQETGEEERFALEILPDMLEKHYGYKLFIPDRDLIPTGTYIEDVA 62
Query: 433 QVMDRCTCVIVLMSTHFMNNSLLHSLTQYAEAKHIDHTIHSKIIPILCSD-----DYFSV 487
+ +D+ +I++M+ +++ +++ T K+I I CS+ +Y V
Sbjct: 63 RCVDQSKRLIIVMTPNYVVRRGWSIFELETRLRNMLVTGEIKVILIECSELRGIMNYQEV 122
Query: 488 GFLQYCVKLK------LNHYASNMEQFWDRLYYSL 516
L++ +KL +FW RL Y +
Sbjct: 123 EALKHTIKLLTVIKWHGPKCNKLNSKFWKRLQYEM 157
>1fyx_A TOLL-like receptor 2; beta-alpha-beta fold, signaling protein;
2.80A {Homo sapiens} SCOP: c.23.2.1 PDB: 1fyw_A 1o77_A
Length = 149
Score = 50.6 bits (121), Expect = 1e-07
Identities = 24/144 (16%), Positives = 50/144 (34%), Gaps = 13/144 (9%)
Query: 386 YDALLLYDEADFDLAKQ-FNTQL--NKMGFTVCDKDNSFLTGQFEHSAFIQVMDRCTCVI 442
YDA + Y E D + +L F + F+ G++ I +++ +
Sbjct: 6 YDAFVSYSERDAYWVENLMVQELENFNPPFKLXLHKRDFIHGKWIIDNIIDSIEKSHKTV 65
Query: 443 VLMSTHFMNNSLLHSLTQYAEAKHIDHTIHSKIIPILCSDD-----YFSVGFLQYCVK-- 495
++S +F+ + ++ + D + I IL L+ +
Sbjct: 66 FVLSENFVKSEWXKYELDFSHFRLFDEN-NDAAILILLEPIEKKAIPQRFXKLRKIMNTK 124
Query: 496 --LKLNHYASNMEQFWDRLYYSLK 517
L+ + E FW L ++K
Sbjct: 125 TYLEWPMDEAQREGFWVNLRAAIK 148
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 45.4 bits (107), Expect = 7e-05
Identities = 33/167 (19%), Positives = 49/167 (29%), Gaps = 65/167 (38%)
Query: 81 MESKQLENSSP----VWELRDNTLNVKPNCRTFVFEKEGHTFGSVITHILQSYPE---VD 133
M L +S VW DN T+G I I+ + P +
Sbjct: 1631 M-GMDLYKTSKAAQDVWNRADNHF--------------KDTYGFSILDIVINNPVNLTIH 1675
Query: 134 FAGYSVPHPADFQIFIRIQVKDGYDSI--DILKKGIKELESACDRITE-----TFNDAMQ 186
F G IR + Y ++ + + G + E I E TF
Sbjct: 1676 FGGEKGKR-------IR----ENYSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRSE-- 1722
Query: 187 CKVILKLT------LLVIQKASKNLRVL-----------VIGSQKHS 216
K +L T L +++KA+ L G HS
Sbjct: 1723 -KGLLSATQFTQPALTLMEKAA--FEDLKSKGLIPADATFAG---HS 1763
Score = 39.6 bits (92), Expect = 0.003
Identities = 34/251 (13%), Positives = 74/251 (29%), Gaps = 91/251 (36%)
Query: 384 AHYDALLLYDE--ADFDLAKQFNTQLNKMGFTVCDKDNSFLTGQFEHSAFIQVMDRCTCV 441
+ DE +L +F +G+ + S + F QV++
Sbjct: 43 EPTEGFAADDEPTTPAELVGKF------LGYVSSLVEPS------KVGQFDQVLN----- 85
Query: 442 IVLMS--THFMNNSLLHSLTQ-------------------YAEAKH-----IDHTIHS-- 473
+ L ++ + +H+L Y A+ D +S
Sbjct: 86 LCLTEFENCYLEGNDIHALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSAL 145
Query: 474 ---------KIIPIL----CSDDYFSVGFLQ--YCVKLKLNHYASNMEQFWDRLYYSLKG 518
+++ I +DDYF L+ Y Y + +L
Sbjct: 146 FRAVGEGNAQLVAIFGGQGNTDDYFEE--LRDLY------QTYHVLVGDLIKFSAETLSE 197
Query: 519 VGKGVPEWDFASNMEQFWDRLYYSLKGVGKGSQKQAIQFQTTPTSMPVAPPDYTLSQQAV 578
+ + + + ++ +G+ +++ P++ P DY L +
Sbjct: 198 LIRTTLDAEK-----------VFT-QGL------NILEWLENPSNTP--DKDY-LLSIPI 236
Query: 579 APPDYTLPQQA 589
+ P + Q A
Sbjct: 237 SCPLIGVIQLA 247
Score = 32.3 bits (73), Expect = 0.58
Identities = 26/152 (17%), Positives = 46/152 (30%), Gaps = 47/152 (30%)
Query: 331 DVYDDCIGFIEEDCLYYENTRLGNSISKNGACMDDPSVITIEDVKSLNLGC-GLAHYDAL 389
DV++ D + + G SI +++P +TI G G +
Sbjct: 1644 DVWNRA------DNHFKDT--YGFSILD--IVINNPVNLTI-----HFGGEKGKRIRE-- 1686
Query: 390 LLYDEADFDLAKQFNTQLNKMGFTVCDKDNSFLTGQFEHSA-------FIQVMDRCTCVI 442
Y F+ + K+ F ++ ++ T F F Q +
Sbjct: 1687 -NYSAMIFETIVDGKLKTEKI-FKEINEHSTSYT--FRSEKGLLSATQFTQP------AL 1736
Query: 443 VLMS----------THFMNNSLL--HSLTQYA 462
LM ++ HSL +YA
Sbjct: 1737 TLMEKAAFEDLKSKGLIPADATFAGHSLGEYA 1768
Score = 32.3 bits (73), Expect = 0.63
Identities = 37/207 (17%), Positives = 53/207 (25%), Gaps = 89/207 (42%)
Query: 211 GSQKHSMMQCRNMDSNHDVEKYRYEDSMDYIKIPIEAIRPKTRQVLNDKLCDIKQLMSPE 270
GSQ+ M MD Y+ S + V N D
Sbjct: 1625 GSQEQGM----GMD--------LYKTS------------KAAQDVWNR--AD-------- 1650
Query: 271 NYQRDYRGLADLMDIKAPPNPNC--------------EDLMKKMFEDWTKSSTLDRSVFN 316
N+ +D G + ++DI NP E+ +FE +F
Sbjct: 1651 NHFKDTYGFS-ILDI-VINNPVNLTIHFGGEKGKRIRENYSAMIFETIVDGKLKTEKIFK 1708
Query: 317 IATFLHFLECIDRFDVYDDCIGFIEEDCLYY-ENTRLGNSISKNGACMDDP-----SVIT 370
H F E+ L + T+ P
Sbjct: 1709 EINE-HSTSYT--FR------S--EKGLLSATQFTQ--------------PALTLMEKAA 1743
Query: 371 IEDVKS---LNLGCGLA-H----YDAL 389
ED+KS + A H Y AL
Sbjct: 1744 FEDLKSKGLIPADATFAGHSLGEYAAL 1770
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna; HET:
CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 35.3 bits (80), Expect = 0.023
Identities = 9/36 (25%), Positives = 17/36 (47%), Gaps = 11/36 (30%)
Query: 602 EKKDSMKKPMLMLTLQNGIRNTLKVFKPNKKKTKAL 637
EK+ ++KK LQ +LK++ + A+
Sbjct: 18 EKQ-ALKK------LQA----SLKLYADDSAPALAI 42
Score = 32.2 bits (72), Expect = 0.21
Identities = 12/41 (29%), Positives = 18/41 (43%), Gaps = 14/41 (34%)
Query: 551 QKQAI-QFQTTPTSMPVAPPDYTLSQQAVAPPDYTLPQQAT 590
+KQA+ + Q S+ + D S AP L +AT
Sbjct: 18 EKQALKKLQ---ASLKLYADD---S----AP---ALAIKAT 45
Score = 29.5 bits (65), Expect = 1.7
Identities = 11/40 (27%), Positives = 15/40 (37%), Gaps = 15/40 (37%)
Query: 48 EEQQLKPGLEQWCFCFSI----PTSTSSVNTSLCIN-YME 82
E+Q LK L+ S+ S +L I ME
Sbjct: 18 EKQALKK-LQA-----SLKLYADDSAP----ALAIKATME 47
Score = 29.5 bits (65), Expect = 1.8
Identities = 10/45 (22%), Positives = 17/45 (37%), Gaps = 24/45 (53%)
Query: 164 KKGIKELESACDRITETFNDAMQCKVILKL------TLLVIQKAS 202
K+ +K+L+++ LKL L I KA+
Sbjct: 19 KQALKKLQAS-----------------LKLYADDSAPALAI-KAT 45
>2of5_H Leucine-rich repeat and death domain-containing protein; death
domain complex, apoptosis; 3.20A {Homo sapiens}
Length = 118
Score = 31.4 bits (71), Expect = 0.26
Identities = 15/109 (13%), Positives = 38/109 (34%), Gaps = 15/109 (13%)
Query: 250 PKTRQVLNDKLCDIKQLMSPENYQRDYRGLA--------DLMDIKAPPNPNCEDLMKKMF 301
+T + L + + D+ +A ++ I+ + ++ ++ M
Sbjct: 6 AETGFLTQSNLLSVAGRLG-----LDWPAVALHLGVSYREVQRIRHEFRDDLDEQIRHML 60
Query: 302 EDWTKSSTLDRSVFNIATFLHFLECIDRFDVYDDCIGFIEEDCLYYENT 350
W + + + LE DR DV ++ +E Y+++
Sbjct: 61 FSWAERQ--AGQPGAVGLLVQALEQSDRQDVAEEVRAVLELGRRKYQDS 107
>3u30_A Ubiquitin, linear DI-ubiquitin; immune system; 2.43A {Homo sapiens}
Length = 172
Score = 29.6 bits (66), Expect = 1.9
Identities = 22/126 (17%), Positives = 48/126 (38%), Gaps = 9/126 (7%)
Query: 128 SYPEVDFAGYSVPHPADFQIFIR------IQVK-DGYDSIDILKKGIKELESACDRITET 180
S+ + VP + QIF++ I ++ + D+I+ +K I++ E
Sbjct: 4 SHHHHHHSSGLVPRGSHMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRL 63
Query: 181 FNDAMQCKVILKLTLLVIQKASKNLRVLVIGSQKHSMMQCRNMDSNHDVEKYRYEDSMDY 240
Q + L+ IQK S V+ + + + + + D+++
Sbjct: 64 IFAGKQLEDGRTLSDYNIQKESTLHL--VLRLRGGMQIFVKTLTGKTITLEVEPSDTIEN 121
Query: 241 IKIPIE 246
+K I+
Sbjct: 122 VKAKIQ 127
>3c7a_A Octopine dehydrogenase; L) stereospecific opine dehydrogenas,
oxidorecutase, oxidoreductase; HET: NAD; 2.10A {Pecten
maximus} PDB: 3c7c_B* 3c7d_B* 3iqd_B*
Length = 404
Score = 29.4 bits (65), Expect = 3.5
Identities = 14/123 (11%), Positives = 28/123 (22%), Gaps = 16/123 (13%)
Query: 444 LMSTHFMNNSLLHSLTQYAEAKHIDHTIHSKIIPILCSDDYFSVGFLQYCVKLKLNHYAS 503
+ M+ S +H + D + F G Q +
Sbjct: 200 FLEMLIMSYSFVHPAILFGRWGSWDGKPVPEA-------PLFYQGIDQATADM------- 245
Query: 504 NMEQFWDRLYYSLKGVGKGVPEWDFASNMEQF-WDRLYYSLKGVGKGSQKQAIQFQTTPT 562
+ + + P D + + + W YY AI +
Sbjct: 246 -LTACSNECKDVANAIMAACPGNDLSDVKDIYQWYLEYYHEDIQDDHDLYHAITTNKSYK 304
Query: 563 SMP 565
+
Sbjct: 305 GLV 307
>2cxh_A Probable BRIX-domain ribosomal biogenesis protein; 18S rRNA, IMP4,
U3 snoRNP, ribosomal biogenesis binding, structural
genomics, NPPSFA; 1.80A {Aeropyrum pernix} SCOP:
c.51.1.2
Length = 217
Score = 28.0 bits (62), Expect = 8.7
Identities = 2/36 (5%), Positives = 7/36 (19%)
Query: 115 GHTFGSVITHILQSYPEVDFAGYSVPHPADFQIFIR 150
F L+ + + + +
Sbjct: 155 ADAFVIAFHARLKPPEAAGYVEAVIESLDARTVAVT 190
>3tm8_A BD1817, uncharacterized protein; HD-GYP, phosphodiesterase, unknown
function, hydrolase,signa protein; 1.28A {Bdellovibrio
bacteriovorus} PDB: 3tmb_A 3tmc_A 3tmd_A
Length = 328
Score = 28.2 bits (63), Expect = 9.4
Identities = 7/33 (21%), Positives = 12/33 (36%)
Query: 218 MQCRNMDSNHDVEKYRYEDSMDYIKIPIEAIRP 250
M + +H MDY+ I + +R
Sbjct: 1 MGSSHHHHHHSSGLVPRGSHMDYVSIRVSTLRG 33
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.320 0.134 0.403
Gapped
Lambda K H
0.267 0.0695 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 9,567,271
Number of extensions: 565459
Number of successful extensions: 1156
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1140
Number of HSP's successfully gapped: 30
Length of query: 639
Length of database: 6,701,793
Length adjustment: 100
Effective length of query: 539
Effective length of database: 3,909,693
Effective search space: 2107324527
Effective search space used: 2107324527
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 60 (27.0 bits)